One of Britain's most prized world heritage sites, the remote islands of St Kilda, will be threatened by vandalism, storm damage and alien species if a missile testing base is closed down, a leading heritage charity has warned.

The National Trust for Scotland said it was dismayed by proposals from the Ministry of Defence to withdraw all 12 staff from its small base on the main island of St Kilda as part of cuts at a missile testing range based in the Outer Hebrides.

Largely uninhabited since the islands' last 36 residents were evacuated in 1930, after centuries of continuous occupation, St Kilda is now Britain's only place to have two world heritage site designations from Unesco, for its archaeology dating back to the iron age, and its birdlife.

The NTS said the MoD personnel, who are stationed on the main island of Hirta to monitor missile tests from Benbecula 41 miles away on the Western Isles, played a crucial role in deterring visits from uninvited ships, monitoring storm damage or spotting alien species that could damage its very vulnerable ground-nesting birds.

St Kilda was involved in a significant scare in February 2008 after a trawler ran aground in heavy storms, potentially allowing rats to colonise the islands. The NTS sent over specialist rat catchers to ensure its gannets, fulmars, puffins and guillemot were safe. No rats were found.

The islands, which include dramatic cliffs and sea stacks, are regarded as north-eastern Europe's most important seabird colony: about half a million birds nest there, including the world's largest northern gannet population, as well as Manx shearwater, storm petrel and Leach's petrel.

If the MoD base is left unmanned, the NTS, now faced with its most severe financial crisis in its history, would have to employ a full-time keeper for the island.

Kate Mavor, the trust's chief executive, urged the MoD to reconsider its plans. "Without the support of the MoD and the infrastructure that they have in place there, there is no doubt that we would find it very difficult to give St Kilda the level of care and attention that it requires.

"However, of more concern is the risk that this proposal poses to the environmental and cultural treasures which make St Kilda so special."

The MoD said todayit wants to cut 150 posts from the missile testing range based at Benbecula, South Uist and St Kilda and an underwater submarine testing facility at Raasay near Skye, as part of £50m savings it needs to make.

Quentin Davies, minister for defence equipment, said: "I know that this will be very disappointing news for the staff at our ranges, and I do not underestimate the impact these proposals and job losses will have on the Hebrides community, especially in the recession."

The area's MSPs, economic development agency and local authorities attacked the decision. Highland and Islands Enterprise's chairman Willie Roe said the loss of 150 jobs would be a "devastating blow" to the Hebridean economy.

The sites' operator, the private defence contractor Qinetiq, was the islands' largest private employer. "We believe these plans fail to take account of the sites' value and we will be doing everything in our power to find a way to put pressure on the MoD and its operator QinetiQ to seek another option," Roe said.